Thanks for the reply zacsmumme. I haven't tried doing shh/pat or putting pressure on his tum to get him through it.
As for the medication, we haven't started it. My DH and I took him to an osteopath, and that really helped. He's eating better, and his A time is much calmer, it's just the 45 min napping. Most of the time, he wakes and is in a great mood, so could that mean he's just a short napper and that's all he needs? He gets tired around the hour-fifteen to hour and a half mark and I put him down again.
Also, he only eats for about 10 min at a time, so he's eating every 2 hours as well. From what I've read, and been told by the dr. and others, it's better to feed him small amounts more often b/c of the reflux. He still gags and chokes but not nearly as much as before. I'm also off of dairy and soy and the usual beans, onions, garlic, etc. That has helped as well. He doesn't wake up to eat.
He still thrashes about in his sleep, but it doesn't seem to be from discomfort as he'll trash, and calm down, never waking.